Personal tools

Sections

Software

Software developed by the Biomodeling & Biosystems Analysis group

For our computational research on collective cell behavior during biological development, we routinely develop simulation codes that we are releasing as open source. If you want to model plant tissues, please use our vertex-based cell-based simulation software VirtualLeaf. If plan to model animal tissues, use Tissue Simulation Toolkit, a two-dimensional implementation of the Cellular Potts Model. Apart from developing our own codes for the Cellular Potts Model, we increasingly make use of the excellent open source package CompuCell3D. The Tissue Simulation Toolkit is a relatively small and straightforward C++ library, making it well suited for developing new ideas and algorithms. CompuCell3D is well suited for constructing new biological models based on existing technology and minor extensions in the form of ``plugins''. Check back soon for releases of CompuCell3D plugins that we have developed in our research.

VirtualLeaf

VirtualLeaf is a cell-based computer-modeling framework for plant tissue morphogenesis. The current version defines a set of biologically-intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. The VirtualLeaf runs on Windows, Mac and Linux.

Overview

VirtualLeaf? is a cell-based computer-modeling framework for plant tissue morphogenesis. The current version defines a set of biologically-intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. The VirtualLeaf runs on Windows, Mac and Linux.